Causing power imbalances within the system for the DC microgrid photovoltaic power generation unit of output volatility and intermittent, the coordinated control strategy of hybrid energy storage system based on DC bus voltage was proposed. The hybrid energy storage system could simultaneously take the advantages of high energy density and high power density. The strategy of the DC link voltage hierarchical control, using four threshold voltage was divided into five regions, with DC bus voltage as the information carrier, determined the operation state of the micro grid system, and realized the free switching between the charging and discharging modes of the hybrid energy storage unit. Hierarchical voltage control could effectively avoid the battery for the normal grid voltage fluctuations and frequent of charge discharge switch, further extending the service life of the battery. Finally, the simulation results of MATLAB/Simulink verified the feasibility of the proposed control strategy.